1 files changed, 92 insertions, 0 deletions
diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make
new file mode 100644
index 000000000000..ead488b0a7d9
--- /dev/null
+++ b/biology/pymol/files/patch-Rules.make
@@ -0,0 +1,92 @@
+--- Rules.make.orig	Wed Apr 30 11:42:37 2003
++++ Rules.make	Wed Apr 30 11:52:50 2003
+@@ -4,42 +4,42 @@
+ #
+ #- Building ----------------------------------------------------------
+ #--- Tell "make" how to get to PyMOL 
+-PYMOL_PATH = /users/warren/pymol
++PYMOL_PATH = ${PREFIX}
+ #---------------------------------------------------------------------
+ #
+ #- Dependencies ------------------------------------------------------
+ #--- X-windows
+-XLIB_DIR = -L/usr/X11R6/lib
+-XINC_DIR = -I/usr/X11R6/include
++XLIB_DIR = -L${X11BASE}/lib
++XINC_DIR = -I${X11BASE}/include
+ #--- Python
+-PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python
++PYTHON_EXE = $(PYMOL_PATH)/bin/python
+ PYTHON_LIB =
+ PYTHON_LIB_DIR = 
+-PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \
+-	-I$(PYMOL_PATH)/ext/include/python2.1/Numeric
++PYTHON_INC_DIR = -I$(PYMOL_PATH)/include/@PYTHON_VERSION@ \
++	-I$(PYMOL_PATH)/include/@PYTHON_VERSION@/Numeric
+ #--- Other external dependencies
+-EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include
+-EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib
++EXT_INC_DIR = -I$(PYMOL_PATH)/include -I.
++EXT_LIB_DIR = -L$(PYMOL_PATH)/lib
+ #---------------------------------------------------------------------
+ #
+-#- Build for LINUX as an importable module ---------------------------
++#- Build for FreeBSD as an importable module ---------------------------
+ #--- System libraries
+-LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -ldl -lpng -lXmu $(ZLIB) -lm
++LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lpng -lXmu $(ZLIB) -lm
+ #--- PyMOL configuration
+ DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY 
+ #--- How we build shared libraries
+ BUILD = -shared 
+ #--- What are we trying to build?
+-DEST = -o modules/pymol/_cmd.so
+-#--- Gcc Options for Linux
+-CCOPT1 = -march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
++DEST = -o modules/_cmd.so
++#--- Gcc Options for FreeBSD
++CCOPT1 = #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
+ #--- libraries for PyOpenGL 
+ PYOGL_LIB =  -lglut -lGL -lGLU -lXmu -lXi
+ #---------------------------------------------------------------------
+ #
+ #- Choose One --------------------------------------------------------
+ #--- GCC Optimized
+-CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer
++CCOPT2 = #-O3 -funroll-loops -fomit-frame-pointer
+ #--- GCC Profiling
+ #CCOPT2 = -pg -O3 -funroll-loops
+ #--- Debugging
+@@ -47,7 +47,7 @@
+ #---------------------------------------------------------------------
+ #
+ #- Choose One --------------------------------------------------------
+-#--- Workaround for XFree86/DRI linux dll problem for module build
++#--- Workaround for XFree86/DRI FreeBSD dll problem for module build
+ BUGS = -D_DRI_WORKAROUND
+ #---
+ #BUGS =
+@@ -69,18 +69,19 @@
+ # No changes normally required below here
+ #---------------------------------------------------------------------
+ 
+-CC = cc
++override CC := ${CC}
+ 
+ LIB_DIRS = $(EXT_LIB_DIR) $(PYTHON_LIB_DIR) $(XLIB_DIR)
+ 
+ # Enable source files to find headers
+ PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \
+-   -I../layer3 -I../layer4 -I../layer5 
++   -I../layer3 -I../layer4 -I../layer5 -I../modules/
+ 
+ C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \
+-   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS)
++   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) $(PYMOL_INC_DIRS)
++
++override CFLAGS := $(C_FLAGS) ${CFLAGS}
+ 
+-CFLAGS = $(C_FLAGS)
+ 
+ 
+